You can debug the result of preprocessing by running doxygen with the -d Preprocessor option. When this option is present, Doxygen will dump the input file to the output after preprocessing has been performed.

I actually found the same solution and was about to post it. Just a note for PREDEFINED the value should be "DEPRECATED(x)=x" with out the quotes it did not give correct results. The link given in your solution was how I found the solution as well. Thanks :)
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gnash117Nov 8 '11 at 20:11

That was the first thing that I tried. If that had worked I would not have posted here. The problem with using the @fn tag is that Doxygen needs to see the function.
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gnash117Nov 8 '11 at 16:09

The @fn tag is so you can separate the documentation from the function. Its not so you can document a function that Doxygen does not think exist. I have tried to change the MACRO_EXPANSION options so that Doxygen would process the DEPRICATED macro before trying to apply the documentation. I think that was the right direction but I could not get it to work.
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gnash117Nov 8 '11 at 16:18